Agricultural soil (Ap-horizon, 0–20 cm) samples were collected in Europe (33 countries, 5.6 million km2) as part of the GEMAS (GEochemical Mapping of Agricultural and grazing land Soil) soil-mapping project. The GEMAS survey area includes diverse groups of soil parent materials with varying geological history, a wide range of climate zones, and landscapes. The soil data have been used to provide a general view of U and Th mobility at the continental scale, using aqua regia and MMI® extractions. The U-Th distribution pattern is closely related to the compositional variation of the geological bedrock on which the soil is developed and human impact on the environment has not concealed these genuine geochemical features. Results from both extraction methods (aqua regia and MMI®) used in this study support this general picture. Ternary plots of several soil parameters have been used to evaluate chemical weathering trends. In the aqua regia extraction, some relative Th enrichment-U loss is related to the influence of alkaline and schist bedrocks, due to weathering processes. Whereas U enrichment-Th loss characterizes soils developed on alkaline and mafic bedrock end-members on one hand and calcareous rock, with a concomitant Sc depletion (used as proxy for mafic lithologies), on the other hand. This reflects weathering processes sensu latu, and their role in U retention in related soils. Contrary to that, the large U enrichment relative to Th in the MMI® extraction and the absence of end-member parent material influence explaining the enrichment indicates that lithology is not the cause of such enrichment. Comparison of U and Th to the soil geological parent material evidenced i) higher capability of U to be weathered in soils and higher resistance of Th to weathering processes and its enrichment in soils; and, ii) the MMI® extraction results show a greater affinity of U than Th for the bearing phases like clays and organic matter. The comparison of geological units with U anomalies in agricultural soil at the country scale (France) enables better understanding of U sources in the surficial environment and can be a useful tool in risk assessments.